Environmental Factor, November 2011, National Institute of Environmental Health Sciences
Genomics Day showcases array and sequencing resources
By Eddy Ball
Gerrish, left, and Bushel watch as Hewitt presents her group's work. Hewitt said she felt fortunate for the bioinformatics and study design support she received at NIEHS. (Photo courtesy of Steve McCaw)
Godfrey's group collaborated with two studies conducted by the University of North Carolina at Chapel Hill that supplied blood samples from cancer cases and healthy controls. (Photo courtesy of Steve McCaw)
Menendez listened to Merrick's presentation, as he waited his turn to speak. Merrick said that NTP has millions of histoglass slides and paraffin tissue blocks that may still be able to yield information for researchers. “I think there are a lot of good reasons to conduct molecular studies on archived material.” (Photo courtesy of Steve McCaw)
NMC research biologist Rick Fannin took a break from his own poster to look at his colleagues' work. (Photo courtesy of Steve McCaw)
Now in its third year and steadily growing, Genomics Day offered intramural researchers a chance to learn about array, sequencing, and bioinformatic resources available through NIEHS and NIH. With high-throughput resources and the output of data from genomic technologies increasing exponentially, Institute scientists are hard pressed to keep abreast of new tools and support in place at NIEHS and through the NIH Intramural Sequencing Center (NISC) in Rockville, Md.
The event Oct. 13 in Rodbell Auditorium was moderated by Kevin Gerrish, Ph.D., technical laboratory manager of the NIEHS Microarray Core (NMC) group headed by Rick Paules, Ph.D., who told the audience, “We have about twice the number of participants we had two years ago.”
As Gerrish pointed out in his introduction, Genomics Day strives to increase awareness and promote discussions of genomics; increase awareness of advances in genomic research; and increase awareness of the scope of bioinformatic support at NIEHS.
As leading-edge biomedical research increasingly uses powerful new technology to generate ever greater volumes of data, scientists need timely information and a network of support to take full advantage of these tools.
Genomics resources in action
The program opened with an overview of microarray resources by Gerrish; an overview of developments in the Next Generation (NextGen) Sequencing group, which has an advance sequencer housed at NISC, by NIEHS senior researcher Paul Wade, Ph.D.; and an introduction to resources and support for bioinformatics/biostatistics from a growing network of specialists, presented by Pierre Bushel, Ph.D., of the NIEHS Biostatistics Branch.
Constituting the heart of the program were presentations by six scientists, selected from the first authors of the 35 posters on display, as part of the afternoon's Genomics Day poster session. These oral presentations demonstrated the advantages of incorporating microarray and NextGen sequencing to advance research in NIEHS labs (see text box).
High volume testing and bioinformatics at NIH
The final two presentations at Genomics Day involved a guided tour of resources at NISC by Robert Blakesley, Ph.D.(http://www.genome.gov/10000785) , director of the Sequencing Group there, as well as an exploration of the applications of whole exome sequencing in cancer and rare diseases by Jim Mullikin, Ph.D.(http://www.genome.gov/11007681) , who is the center director of NISC. NIEHS is a high-volume user of NISC, especially for ChIP-Seq, RNA-Seq, and microRNA-Seq, on the center's six sequencing platforms.
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As he showed slides of the impressive equipment housed in the 7,000 square foot open-space NISC laboratory, Blakesley discussed the management challenges he faces in trying to utilize it all efficiently. “It's difficult to get them all into one picture,” he said of the sheer volume of NISC resources. To keep things running smoothly, all the equipment is mobile, so clusters can be assembled, as required, for specific jobs and projects. “We want to make this a manufacturing space,” he explained.
Like any automated facility, NISC relies on careful quality control software and procedures to balance computational load and disk storage, as well as barcoding everything involved in laboratory and computational analysis. The tremendous bioinformatics load is handled by a Linux cluster with a 900 terabyte disk.
One of the NISC resources that NIEHS has not been using, said Mullikin as he began his talk, is cost-effective and informative exome sequencing. This technique represents an efficient strategy to selectively sequence the coding regions of the genome, to identify novel genes associated with rare and common disorders. Over the course of his talk, Mullikin discussed three projects that illustrated the utility of exome sequencing in cancer and rare disease research.
Volume at NISC is increasing, as the costs of analysis drops. “Things keep changing in the lab,” Mullikin said, pointing to the three exome sequencing platform upgrades performed since March 2010 alone, to achieve progressively greater processing capacity.
Microarray and sequencing research highlighted at Genomics Day
- Permanent records of transient hyper-mutation in yeast and human genomes, using NextGen Sequencing, by Steven Roberts, Ph.D., postdoctoral fellow in the NIEHS Chromosome Stability Group(http://www.niehs.nih.gov/research/atniehs/labs/gisbl/pi/cs/index.cfm). Roberts and colleagues determined a role for single-strand DNA in the formation of mutation clusters characteristic of cancer genomes.
- Whole-genome ERalpha binding in mouse uterine tissue, using Agilent gene expression and ChIP-Seq, by Sylvia Hewitt, senior biologist in the NIEHS Receptor Biology Group(http://www.niehs.nih.gov/research/atniehs/labs/epi/pi/molecular/index.cfm). Hewitt and her team identified regulatory elements controlling genes involved in regulating the estrogen response in the uterus, analyzing the data with bioinformatics support from Bushel.
- Examining miRNA expression in pre- and post-operative lung cancers, using Affymetrix miRNA microarrays, by Ashley Godfrey, Ph.D., postdoctoral fellow in the NIEHS Molecular and Genetic Epidemiology Group(http://www.niehs.nih.gov/research/atniehs/labs/lmc/molecular/staff.cfm). Godfrey and members of her group utilized support from Stella Sieber of the NMC in their search for miRNAs that show altered expression in serum, to use as the basis for a non-invasive test for recurrence in lung cancer patients.
- Use of archival paraffin tissues for qPCR gene expression: correlation with microarray data, using quantitative PCR and formalin-fixed paraffin embedded tissue, by Alex Merrick, Ph.D., head of the NTP Molecular Toxicology and Informatics Group(http://www.niehs.nih.gov/research/atniehs/labs/bmsb/moltox/index.cfm). Merrick and an NTP team of researchers explored the feasibility of mining tissues, archived by NTP from decades of animal testing, to study gene expression.
- A mutagenesis screen to identify transcriptional regulators of metallothionein in Caenorhabditis elegans, using NextGen sequencing, by Julie Hall, Ph.D., postdoctoral fellow in the NTP WormTox Group. Hall and WormTox Group head Jonathan Freedman, Ph.D., used forward and reverse genetics in their search for transcriptional regulators of the gene mtl-1, which is involved in metal detoxification.
- Specific stress and non-stressed conditions can dramatically influence genomic binding and transactivation by p53 in U2OS cancer cells, using Affymetrix gene expression and ChIP-seq, by Daniel Menendez, Ph.D., staff scientist in the NIEHS Chromosome Stability Group(http://www.niehs.nih.gov/research/atniehs/labs/gisbl/pi/cs/index.cfm). With statistical support from members of the NIEHS Systems Biology Group(http://www.niehs.nih.gov/research/atniehs/labs/escbl/pi/systemsbiology/index.cfm), Menendez' team explored the role of p53 binding and gene expression changes in non-stressed and stressed cancer cells.